Bugzilla Bug 216057

Hi,
Like the title says, xdrawchem-1.9.9 fails to build against
openbabel-2.2.0_beta4. I just recompile finish rebuilding my entire system
(emerge -eN system  && emerge -eN world). I provided the error messages in the
Actual result section. Any ideas?

Thanks
Paul

Reproducible: Always

Steps to Reproduce:
1.emerge =sci-chemistry/openbabel-2.2.0_beta
2.emerge =sci-chemistry/xdrawchem-1.9.9
3.

Actual Results:  
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I..  -Wall
-I/usr/X11R6/include -DUNIX -DRINGHOME="\"/usr/share/xdrawchem/\""
-DXDC_SERVER=\"www.xdrawchem.org\" -I/usr/include/openbabel-2.0    -g
-I/usr/qt/3/include -g -march=pentium4 -O3 -pipe -fomit-frame-pointer -MT
application_ob.o -MD -MP -MF ".deps/application_ob.Tpo" -c -o application_ob.o
application_ob.cpp; \
        then mv -f ".deps/application_ob.Tpo" ".deps/application_ob.Po"; else
rm -f ".deps/application_ob.Tpo"; exit 1; fi
application_ob.cpp: In member function 'void
ApplicationWindow::OBGetFilters()':
application_ob.cpp:48: error: 'Formatpos' was not declared in this scope
application_ob.cpp:48: error: expected `;' before 'pos'
application_ob.cpp:51: error: 'GetNextFormat' is not a member of
'OpenBabel::OBConversion'
make[2]: *** [application_ob.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory
`/var/tmp/portage/sci-chemistry/xdrawchem-1.9.9/work/xdrawchem-1.9.9/xdrawchem'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory
`/var/tmp/portage/sci-chemistry/xdrawchem-1.9.9/work/xdrawchem-1.9.9'
make: *** [all] Error 2
 *
 * ERROR: sci-chemistry/xdrawchem-1.9.9 failed.
 * Call stack:
 *               ebuild.sh, line   49:  Called src_compile
 *             environment, line 1029:  Called die
 * The specific snippet of code:
 *       emake || die "emake failed."
 *  The die message:
 *   emake failed.
 *
 * If you need support, post the topmost build error, and the call stack if
relevant.
 * A complete build log is located at
'/var/tmp/portage/sci-chemistry/xdrawchem-1.9.9/temp/build.log'.
 * The ebuild environment file is located at
'/var/tmp/portage/sci-chemistry/xdrawchem-1.9.9/temp/environment'.
 *

 * Messages for package sci-chemistry/xdrawchem-1.9.9:

 *
 * ERROR: sci-chemistry/xdrawchem-1.9.9 failed.
 * Call stack:
 *               ebuild.sh, line   49:  Called src_compile
 *             environment, line 1029:  Called die
 * The specific snippet of code:
 *       emake || die "emake failed."
 *  The die message:
 *   emake failed.
 *
 * If you need support, post the topmost build error, and the call stack if
relevant.
 * A complete build log is located at
'/var/tmp/portage/sci-chemistry/xdrawchem-1.9.9/temp/build.log'.
 * The ebuild environment file is located at
'/var/tmp/portage/sci-chemistry/xdrawchem-1.9.9/temp/environment'.
 *
 * GNU info directory index is up-to-date.


Expected Results:  
completed compilation and installation

emerge --info
Portage 2.1.4.4 (default-linux/x86/2007.0/desktop, gcc-4.2.3, glibc-2.7-r2,
2.6.24-gentoo-r2 i686)
=================================================================
System uname: 2.6.24-gentoo-r2 i686 Intel(R) Pentium(R) 4 CPU 2.80GHz
Timestamp of tree: Fri, 28 Mar 2008 22:30:02 +0000
app-shells/bash:     3.2_p33
dev-java/java-config: 1.3.7, 2.1.5
dev-lang/python:     2.5.1-r5
dev-python/pycrypto: 2.0.1-r6
sys-apps/baselayout: 1.12.11.1
sys-apps/sandbox:    1.2.18.1-r2
sys-devel/autoconf:  2.13, 2.61-r1
sys-devel/automake:  1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.1
sys-devel/binutils:  2.18-r1
sys-devel/gcc-config: 1.4.0-r4
sys-devel/libtool:   1.5.26
virtual/os-headers:  2.6.24
ACCEPT_KEYWORDS="x86 ~x86"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-march=pentium4 -O3 -pipe -fomit-frame-pointer"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config
/usr/kde/3.5/shutdown /usr/share/config"
CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf
/etc/gconf /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/
/etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/terminfo
/etc/texmf/web2c /etc/udev/rules.d"
CXXFLAGS="-march=pentium4 -O3 -pipe -fomit-frame-pointer"
DISTDIR="/usr/portage/distfiles"
FEATURES="ccache cvs distcc distlocks metadata-transfer sandbox sfperms strict
unmerge-orphans userfetch userpriv usersandbox"
GENTOO_MIRRORS="ftp://ftp.nrc.ca/pub/systems/linux/gentoo/
http://mirror.tucdemonic.org/gentoo/
ftp://gentoo.netnitco.net/pub/mirrors/gentoo/source/ 
http://gentoo.netnitco.net ftp://ftp.ussg.iu.edu/pub/linux/gentoo"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress
--force --whole-file --delete --stats --timeout=180 --exclude=/distfiles
--exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/portage/local/layman/science /usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X aac aalib acl acpi alsa ansi arts berkdb cairo cdr cli cracklib crypt
cups dbus divx4linux dri dvd dvdr dvdread eds emboss encode esd evo faad2 fam
fbdev firefox flac fortran gcj gdbm gif gnome gpm gstreamer gtk hal iconv ipv6
isdnlog java jpeg kde kerberos ldap live m4a mad midi mikmod mp3 mp4 mpeg
mudflap nas ncurses network nls nptl nptlonly ogg opengl openmp oss pam pcre
pdf perl png pppd python qt3 qt3support qt4 quicktime readline reflection sdl
seamonkey session spell spl ssl svg tcpd tiff truetype unicode vorbis
win32codecs wma wmv x86 xml xorg xv zlib" ALSA_CARDS="ali5451 als4000 atiixp
atiixp-modem bt87x ca0106 cmipci emu10k1 emu10k1x ens1370 ens1371 es1938 es1968
fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx
via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop
empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mulaw multi
null plug rate route share shm softvol" APACHE2_MODULES="actions alias
auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm
authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache
dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache
filter headers include info log_config logio mem_cache mime mime_magic
negotiation rewrite setenvif speling status unique_id userdir usertrack
vhost_alias" ELIBC="glibc" INPUT_DEVICES="keyboard mouse" KERNEL="linux"
LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses
text" USERLAND="GNU" VIDEO_CARDS="vesa vga fbdev nv nvidia"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL,
LDFLAGS, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS,
PORTAGE_RSYNC_EXTRA_OPTS

Created an attachment (id=148423) [edit]
The build log

Here is the complete build log

Thanks much for your bug report. Unfortunately, it looks like
there's quite a bit of breakage with openbabel-2.2.0. I'll have
a look but this may be quite difficult to fix.

best,
Markus

I've changed the dependencies to <openbabel-2.2 for
now until we've sorted this out. openbabel-2.0 and 2.1
seem to work fine for me.

Markus

fwiw I've been working on openbabel as much as I can, it's a can of worms.

cryos is one of the openbabel devs (I think) and I'll
email him later to ask how to best replace the
GetNextFormat API function that is missing in 
openbabel-2.2 and causes the xdrawchem compile to
bomb. It should be fairly trivial for somebody who 
knows the openbabel API I would assume. If he doesn't
know, I can probably fix it myself, since xdrawchem's
upstream seems pretty dead.

cheers,
Markus

Only just come across this - I will take a look and see what I can do.

Could you elaborate on the breakage in 2.2 too? We are working on getting the
2.2 release out and obviously I would like to correct any breakage before the
release if possible. The API should not be broken and where it is I will see
about correcting that (or talking to the people who can).

Take a look at openbabel-2.2.0_beta4-r1 and the patch it applies - fixes it
here. If it looks good I will see about getting this applied upstream before
the release of OpenBabel 2.2. Please do let me know about any other issues with
OpenBabel 2.2 too.

Hi Marcus,

I just peeked at your api patch in openbabel-2.2.0_beta4-r1
and it looks like it contains exactly what what missing 
before, i.e. the member definition for GetNextFormat.
I haven't tried compiling xdrawchem yet, but I think this should
fix it.

Thanks much,
Markus

Between Chris Morley and myself upstream is now patched in a slightly different
way. Hopefully there will be another beta release very soon, if not I might do
a snapshot.... Now is the time to let me/the OpenBabel community know about any
issues before the 2.2 release. If you know of any other problems I would really
appreciate you letting me know sooner rather than later.

Hopefully everything else looks good and there are no more API breaks.

Hi Marcus,

xdrawchem builds fine for me against openbabel-2.2.0_beta-r1.
Thanks!

The only additional issue with openbabel I am aware of is #212526 
but I haven't looked into it enough to be able to judge if it is 
a problem with openbabel's build system in general or gentoo specific.

Best,
Markus

I'm thinking of bugs #212212 and #206574.

Should I file this as a separate bug, or is it being here enough?

config.status: executing depfiles commands
config.status: executing include/openbabel/babelconfig.h commands
Makefile:156: *** missing separator.  Stop.
 * 
 * ERROR: sci-chemistry/openbabel-2.2.0_beta4-r1 failed.
 * Call stack:
 *               ebuild.sh, line   49:  Called src_compile
 *             environment, line 2176:  Called die
 * The specific snippet of code:
 *           emake || die "emake failed";
 *  The die message:
 *   emake failed
 * 
 * If you need support, post the topmost build error, and the call stack if
relevant.
 * A complete build log is located at
'/var/tmp/portage/sci-chemistry/openbabel-2.2.0_beta4-r1/temp/build.log'.
 * The ebuild environment file is located at
'/var/tmp/portage/sci-chemistry/openbabel-2.2.0_beta4-r1/temp/environment'.
 * 

Shingoshi

Created an attachment (id=151797) [edit]
Build.log and emerge --info

This is the wx-widgets wx-config problem. It is in a separate bug (forget which
one right now and am on the way out the door). You can run wx-config to fix
this one, this should get fixed in the next release.

This should be fixed in openbabel-2.2.0.

Thanks,
Markus